Cell type annotation

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PsychENCODE’s marker gene selection might be imperfect since some “marker” genes are shared by different cell types. However, it has enough discriminatory power. Using this initial dictionary of marker genes, we can start analyzing 10x data, which consist of these three files:
## %%MatrixMarket matrix coordinate integer general
## 17926 70634 119696200
## 56 1 1
## 139 1 1
## 270 1 1
## 324 1 1
## 375 1 1
## 389 1 1
## 420 1 1
## 557 1 1
## AAACGGGAGATCCCGC.1
## AAATGCCTCCAATGGT.1
## AACCATGTCAGTGCAT.1
## AACCATGTCTGTACGA.1
## AACCGCGTCCGCATAA.1
## AACGTTGGTTCAGGCC.1
## AACTGGTGTACCGGCT.1
## AAGACCTAGTTAACGA.1
## AAGGAGCAGCAATCTC.1
## AAGGAGCTCTGCTGCT.1
- Gene/feature list (these names should exist in the marker file):
## FO538757.2
## SAMD11
## NOC2L
## KLHL17
## PLEKHN1
## PERM1
## HES4
## ISG15
## AGRN
## RNF223

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Basic statistics for cell type annotation

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- 1,472 cells per individual: 50.9% (N=745 \(\pm\) 388) cells for Ex, 12.23% (N=179 \(\pm\) 103) cells for In, 3.54% (N= 54 \(\pm\) 35) cells for OPC, 0.33% (N= 4 \(\pm\) 5) cells for Endo, 25.22% (N=380 \(\pm\) 252) cells for Oligo, 2.61% (N= 36 \(\pm\) 25) cells for Microglia, 4.95% (N= 71 \(\pm\) 47) cells for Astro, 0.34% (N= 4 \(\pm\) 4) cells for Per on average.
Correlation with the annotations of Mathys et al.

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Marker genes are associated with the AD phenotype

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Differential expression analysis
A table for genes significant at FWER 1%
What if cell types were combined? Cell-type-sorted pseudo-bulk analysis improves statistical power
## Joining, by = "ct"

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CoCoA identified 377 genes are differentially-regulated between different AD conditions
377 genes (2.72%) consist of 123 found in Ex, 36 found in In, 86 found in Oligo, 58 found in OPC, 24 found in Microglia, 57 found in Astro
28 genes (0.2%) consist of 5 found in Ex, 4 found in In, 6 found in Oligo, 6 found in OPC, 2 found in Microglia, 5 found in Astro
13848 genes in total.

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## quartz_off_screen
## 2
p-value distribution
Why do we find more genes with CoCoA?
Take the examples of Microglia genes
## Loading required package: cba
## Loading required package: proxy
##
## Attaching package: 'proxy'
## The following objects are masked from 'package:stats':
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## as.dist, dist
## The following object is masked from 'package:base':
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## as.matrix


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Confounding effects prevalent…

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## Warning: Removed 4702 rows containing non-finite values (stat_smooth).
## Warning: Removed 4702 rows containing non-finite values (stat_cor).
## Warning: Removed 4702 rows containing missing values (geom_point).

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Gene ontology enrichment

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Up-regulated DEGs (2,092 genes)

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Down-regulated DEGs (2,317 genes)

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GO enrichment for each cell type
DEGs up-regulated (956 genes)

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A table for the GO keywords enriched by the up-regulated genes
DEGs down-regulated (1,044 genes)

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A table for the GO keywords enriched by the down-regulated genes